DOI: 10.18129/  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see hermes.

Preprocessing, analyzing, and reporting of RNA-seq data

Bioconductor version: 3.16

Provides classes and functions for quality control, filtering, normalization and differential expression analysis of pre-processed RNA-seq data. Data can be imported from `SummarizedExperiment` as well as `matrix` objects and can be annotated from BioMart. Filtering for genes without too low expression or containing required annotations, as well as filtering for samples with sufficient correlation to other samples or total number of reads is supported. The standard normalization methods including `cpm`, `rpkm` and `tpm` can be used, and `DESeq2` as well as `voom` differential expression analyses are available.

Author: Daniel Sabanés Bové [aut, cre], Namrata Bhatia [aut], Stefanie Bienert [aut], Benoit Falquet [aut], Haocheng Li [aut], Jeff Luong [aut], Lyndsee Midori Zhang [aut], Simona Rossomanno [aut], Tim Treis [aut], Mark Yan [aut], Naomi Chang [aut], Chendi Liao [aut], Carolyn Zhang [aut], Joseph N. Paulson [aut]

Maintainer: Daniel Sabanés Bové <daniel.sabanes_bove at>

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biocViews DifferentialExpression, Normalization, Preprocessing, QualityControl, RNASeq, Software
Version 1.2.0
In Bioconductor since BioC 3.15 (R-4.2) (1 year)
License Apache License 2.0 | file LICENSE
Depends ggfortify, R (>= 4.1), SummarizedExperiment(>= 1.16)
Imports assertthat, biomaRt, Biobase, BiocGenerics, checkmate (>= 2.1), circlize, ComplexHeatmap, DESeq2, dplyr, edgeR, EnvStats, forcats, GenomicRanges, ggplot2, ggrepel (>= 0.9), IRanges, lifecycle, limma, magrittr, matrixStats, methods, MultiAssayExperiment, purrr, R6, Rdpack, rlang, stats, S4Vectors, tidyr, utils
Suggests BiocStyle, DelayedArray, DT, grid, httr, knitr, rmarkdown, statmod, testthat (>= 2.0), vdiffr, withr
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